Molecular Graphics: Bridging Structural Biologists and Computer Scientists

Abstract

Visualization of molecular structures is one of the most common tasks carried out by structural biologists, typically using software, such as Chimera, COOT, PyMOL, or VMD. In this Perspective article, we outline how past developments in computer graphics and data visualization have expanded the understanding of biomolecular function, and we summarize recent advances that promise to further transform structural biology. We also highlight how progress in molecular graphics has been impeded by communication barriers between two communities: the computer scientists driving these advances, and the structural and computational biologists who stand to benefit. By pointing to canonical papers and explaining technical progress underlying new graphical developments in simple terms, we aim to improve communication between these communities; this, in turn, would help shape future developments in molecular graphics.

Network Pharmacology Prediction and Molecular Docking-Based Strategy to Discover the Potential Pharmacological Mechanism of Huai Hua San Against Ulcerative Colitis

“…Docking models with the lowest binding affinity were visualized and hydrogen bonds were displayed by Pymol (3D) and LigPlus (2D), both of which have been widely applied to visualize the docking results including docking site and hydrogen-bond interaction patterns between the ligand and the main-chain or side-chain elements of the protein. 50,51 Cell Culture 3260 medium supplemented with 10% fetal bovine serum, 100μg/mL streptomycin, and 100U/mL penicillin, at 37°C with 5% CO 2 and 95% air.…”

The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects

“…While many freeware visualization tools have been proposed in the computational chemistry field by enjoying the progresses experienced by computer graphics, (Martinez et al, 2019) very few freeware pieces of software include features which go beyond the simple graphical analysis. Indeed the available resources rarely comprise tools by which one may perform every phase of a molecular modeling study from the design and preparation of the molecular structures to the analysis of the generated results.…”

Visualizing protein structures — tools and trends

“…There still exists a huge potential for substantial improvements of visualization methods by better integration of different scientific communities, in particular computer scientists involved in the field of computer graphics and biologists with visualization needs. Much untapped potential can be found in exciting new methodologies developed in computer science that do not or only slowly transfer into tools accessible to structural biologists as described in more detail in [3]. Among the upcoming new challenges in visualization that would benefit from such integration, we may mention for instance the depiction of uncertainty, see [74] for a recent exploration of this topic, or how to capture the dynamics governing macromolecules in static pictures (briefly discussed in [3] as well).…”

“…Significant contributions originate in the computer science field of computer graphics. These contributions may only slowly transfer to the field of structural biology [3] as this process requires available end-user oriented software tools for efficient dissemination. Such tools are at the core of this survey.…”